BTN3A2

butyrophilin subfamily 3 member A2, the group of V-set domain containing|Butyrophilins

Basic information

Region (hg38): 6:26365158-26378320

Links

ENSG00000186470 ∙ NCBI:11118 ∙ OMIM:613594 ∙ HGNC:1139 ∙ Uniprot:P78410 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BTN3A2 gene.

• Inborn genetic diseases (12 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTN3A2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			10	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	10	2	3

Variants in BTN3A2

This is a list of pathogenic ClinVar variants found in the BTN3A2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-26368198-T-A		not specified	Uncertain significance (Jun 24, 2022)
6-26368621-G-A		not specified	Uncertain significance (Jan 10, 2022)
6-26368645-C-G		not specified	Uncertain significance (May 02, 2023)
6-26368649-C-A		not specified	Likely benign (Feb 02, 2022)
6-26368710-C-T			Benign (Dec 05, 2017)
6-26368711-G-A		not specified	Uncertain significance (Nov 21, 2022)
6-26368772-C-T		not specified	Uncertain significance (Aug 15, 2023)
6-26368829-C-T		not specified	Uncertain significance (Feb 15, 2023)
6-26368841-G-A		not specified	Uncertain significance (Apr 04, 2023)
6-26370382-A-C		not specified	Uncertain significance (Nov 10, 2022)
6-26370433-C-A		not specified	Uncertain significance (Sep 20, 2023)
6-26370550-T-A		not specified	Uncertain significance (Jun 05, 2023)
6-26370570-G-A		not specified	Likely benign (Nov 18, 2022)
6-26370605-T-G			Benign (Apr 27, 2020)
6-26372914-G-A		not specified	Uncertain significance (Nov 06, 2023)
6-26372926-A-G		not specified	Uncertain significance (Feb 27, 2024)
6-26372971-G-A		not specified	Uncertain significance (Feb 13, 2023)
6-26372978-C-T		not specified	Uncertain significance (Oct 20, 2023)
6-26374342-C-G		not specified	Uncertain significance (Jan 10, 2022)
6-26374343-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BTN3A2	protein_coding	protein_coding	ENST00000356386	7	13160

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.10e-10	0.0924	116526	230	8992	125748	0.0374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.575	158	180	0.879	0.00000972	2135
Missense in Polyphen		48	53.932	0.89002		714
Synonymous	0.640	65	71.9	0.904	0.00000440	661
Loss of Function	0.259	16	17.2	0.933	9.72e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0991	0.0986
Ashkenazi Jewish	0.0542	0.0544
East Asian	0.00371	0.00370
Finnish	0.0121	0.0121
European (Non-Finnish)	0.0416	0.0412
Middle Eastern	0.00371	0.00370
South Asian	0.0485	0.0480
Other	0.0435	0.0436

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in T-cell responses in the adaptive immune response. Inhibits the release of IFNG from activated T-cells. {ECO:0000269|PubMed:21918970, ECO:0000269|PubMed:22767497}.
• Pathway: Butyrophilin (BTN) family interactions;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0717

Intolerance Scores

• loftool: 0.836
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.49

Haploinsufficiency Scores

• pHI: 0.0649
• hipred: N
• hipred_score: 0.187
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0425

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: T cell mediated immunity;regulation of immune response;T cell receptor signaling pathway;interferon-gamma secretion
• Cellular component: plasma membrane;external side of plasma membrane;membrane;integral component of membrane
• Molecular function: signaling receptor binding